Stranded
by The 11th Doctor's Mermaid Sam
Summary: Sheppard went to bed on Atlantis and woke up on Destiny. He doesn't know how or why. All he does know is that Atlantis is in danger, without his help, could be doomed.  So how was he stuck on a ship he didn't even know about, millions of light years away.
1. Prologue

Hello there =D Thanks for reading, this story will be a multi chapter fic, and it _should _be updated regularly.

Don't hold me to it though, because I'm in Year 11 and coursework is trying to get the better of me =d. Failing French and loads of German coursework for History. =D Thankfully it's a subject I like.

If there is anybody reading my other Stargate Atlantis multi fic, The Hetta Chronicles, I'm sorry I haven't updated it in a while, I've just been struggling with how to characterise Hetta, I think I'm making her a bit...weak. And I'm just trying to figure it out a bit, but rest assured, it will be updated soon =D

Onto the story then Thanks again for reading

XXX

Summery.

_John Sheppard went to bed on Atlantis and woke up on The Destiny. He doesn't know how, or why. All he does know is that Atlantis is in danger and without his help, it could be doomed. So how was he stuck on a ship he didn't even know about, millions of light years away from home?_

XXX

John Sheppard groaned, dropping onto the bed in his quarters. The Asuran threat that Atlantis was under was bad, they had three Asuran ships coming to destroy Atlantis, the good thing was that they were six weeks away so they had time to prepare and plan.

John sighed, and fell asleep thinking of the dreamless sleep he wouldn't get.

XXX

John was woken roughly, being shaken by a soldier. 'What's happening?' he asked sleepily, alertness not yet reaching him.

Sir, we have an intruder.' A voice hit his ears. 'We just found him asleep in the corridor, doesn't even look like he knows where he is.'

'Where am I? He asked, not showing his slight fear. 'Last thing I knew, I was falling asleep on Atlantis.'

'Atlantis?' the soldier said in amazement. 'In the Pegasus Galaxy?'

'Yeah.' John said in annoyance. 'How the hell did I get here?'

'You're on the good ship Destiny.' The man said. 'I'm Sergeant Ronald Greer. I presume that you're Colonel John Sheppard?'

John stood up, cracking his knee loudly and wincing. 'You presume correctly Sergeant.'

'This way Sir.' Greer indicated. 'I'll take you to Colonel Young.'

John followed him down the corridor.


	2. Colonel Young, Atlantis?

Chapter two! Here we go =D Thanks for reading.

XXX

Greer showed Sheppard into the Destiny gate room and John had to swallow the gasp that rose up in his throat.

'It's amazing.' He said slowly, and lowly.

Greer watched him, smiling under his breath. 'Colonel Young is this way.'

John nodded, still amazed and silenced by the prototype gate. 'Yeah,' he said awestruck.

Greer led him to a side room, where John locked eyes with Colonel Young. 'Sir.' He saluted sloppily.

Young surveyed him, before asking 'Colonel Sheppard?'

John nodded, staying silent.

'Why are you here?' Young asked. 'In your own body?'

'I don't know.' John shrugged. 'I went to sleep on Atlantis and woke up in the hallway with Greer poking me with a gun.'

Young nodded, 'You'll need to talk to Rush and Eli.'

'And where are they?' John asked.

'Sergeant Greer or Lieutenant Scott will escort you to them.' Young told him.

John nodded and followed Greer out of the room.

They were walking through the hall when John looked at Greer and asked 'Who's Rush and Eli?'

Greer sneered. 'Rush is the "best" scientist Destiny has, but he's been terrible, manipulative and vile. Eli is basically his assistant, most people see him as sweet, but he's really naive.'

John nodded, before Greer stopped him in front of a door. 'This is them.'

John nodded at him. 'Thanks Sergeant.' Before walking in and being met by two people, one set of eyes on him and the other on a consol.

'Hello.' He said, smiling at the overweight man, staring at him wearing a red T-Shirt emblazoned You Are Here.

'Eli.' The other person introduced himself, 'Also called Mathboy.' He smiled nervously, before looking behind him. 'Rush!'

'What do you want Eli?' the older man said wearily.

'We have a visitor.' He said promptly.

Rush looked up from the consol he was working at and shock enveloped his face. 'Colonel Sheppard! What are you doing here?' he said, practically running over to him.

'I don't actually know how I got here.' John said nervously.

'Well what happened?' Rush asked sceptically.

'I went to sleep on Atlantis and I woke up in the corridor.' John repeated.

'Hmmm.' Rush murmured, before walking around the room.

John was quickly getting bored with Rush's monologue and started talking to Eli. 'So, what's it like on Destiny?'

Eli smiled at him gently. 'It's ... different.'

John smiled at him, 'It was the same with Atlantis in the beginning. I couldn't get used to the sea sounds.'

Eli grinned, 'You wanna go to the mess? They have the protein slop they always serve.'

John nodded.

Eli led him out of the room, leaving Rush to figure out his problem.

XXX

Three days later, and John got on with most people on the ship, mainly Eli, Colonel Young and Sergeant Greer.

This particular day, Eli and Greer was on the planet below the ship that Destiny had dropped out of FTL above, so he was alone in the Destiny Mess when Rush sat at the table and started talking to him.

'So, I think I figured it out.' He said, making John look at him.

'And?' he prompted.

'I think that Atlantis, because she is a sentient ship mainly, sensed that this ship was in danger and sent the most qualified person she knew to help it.' Rush said.

'Well, Atlantis was in danger as well.' John said. 'The Asuran's have launched an attack on Atlantis, they get there in five weeks.'

'Maybe the danger on Destiny is more urgent?' Rush suggested, but John had stopped listening because he saw something different. He could see the Atlantis infirmary.

Rodney and Carson were standing there, arguing.

'He's got to be somewhere!' Rodney yelled.

'I know that Rodney.' Carson said wearily, 'But he just disappeared.'

'Umm, guys?' he said, interrupting them.

'Sheppard!' Rodney nearly screamed. 'Where are you?'

'I'm on the Destiny.' John said.

'The ship Destiny?' Rodney asked. 'How the hell did you get there?'

'Well, Rush theorised that Atlantis sensed that the Destiny was in danger and sent the most qualified person that she knew to the Destiny.' John surmised.

'Are you ok Colonel?' Carson questioned.

'Yeah I'm fine, except for the vision of you here.' He quipped before wincing, and bringing his hand to his head.

'Colonel!' 'Sheppard!' were yelled at the same time and John closed his eyes to stop the dizzy feeling, and opened his eyes to see Rush leaning over him 'Colonel?' he asked worriedly, looking him over. 'Are you ok?'

'Where's Carson gone?' he said woozily. 'Rodney and Carson were here a second ago?'

'No Colonel Sheppard,' Rush contradicted. 'You haven't left the Destiny Mess hall, you collapsed a moment ago.'

'I went to Atlantis.' He mumbled, before passing out.

XXX

John struggled to open his eyes, and in the end he gave up the struggle and left them closed just listening to the sounds of the ship around him.

'_Could he be suffering aftermaths of the transport?'_

'_No, I don't think so,' a female answered. 'I think it's more the fact that Atlantis has sent his body and mind here, and the connection is fracturing, and Atlantis can't control the link.'_

'_They have a ZPM.' Rush argued._

'_Colonel Young!' TJ said, or John was pretty sure it was TJ, she was the only medic here, 'he'll be waking up soon so if you need to talk to him, now would be good.'_

'_Okay.' John could hear the nod in his voice. 'I'm going.'_

John sat up, wincing slightly, at watched at Colonel Young walked over to him.

'Colonel Sheppard.' He said. 'How are you feeling?'

John shrugged, 'I'm fine.'

Young nodded. 'Rush said you told him you went to Atlantis.'

John nodded. 'I did.'

Young surveyed him. 'Do you know how you got there?'

John suppressed the urge to roll his eyes. 'No. I'm pretty sure Rush will find out for you, and Rodney will be looking it up now.'

Young nodded. 'Well if there's nothing you can tell me, I'll be back to the Gate room, there's a team expected back.'

John nodded at him before spying Rush staring at him over his shoulder. They met each other's gaze and regarded each other, silently promising that eventually, they would understand each other.

**XXX**

**Righhttttt, =d Not totally happy with this chapter, not sure where I was going with it, or where exactly the storyline is going, I originally started this as Eli and John, hurtling through space, trapped on ships the opposite sides of the galaxy, but then again, where do storylines take you? **

**Chapter three, will be up soon =D**

**Thanks you reading**

**Emily.**


	3. Eli

**Here'ssss Chapter 3!**

**Thanks you reading =D**

**XXX**

TJ let John out the next day, and the first thing he did was ask Lieutenant Scott where his quarters were.

Scott had smiled at him and led him to a bare room near to the Gate room, which he had promptly left him at smiling. 'I'll leave you to get acquainted Sir.' Scott had said before leaving the room quickly.

John looked around the bare room, the bunks set into the wall like the drilling station they had found. Quite small, but John decided that he could come to like it quite quickly.

He sat in the middle of the room, facing the door, and sat in the meditative stance that Teira had taught him, in the time he had been stuck in the Sanctuary.

Hours later, he opened his eyes, and saw Eli standing there watching him.

'Yes?'

'What were you doing?' Eli asked him, indicating with his hands where John had been sitting a moment ago.

'Meditating.' John said, 'I got stuck in a time dilation field and the people there taught me how.'

Eli nodded, looking slightly freaked out. 'Umm, Colonel Young wanted you.'

John nodded, and walked out of the door. 'Lead the way.' He said, looking back at the scientist.

XXX

'WE NEED HIM HERE!'

'HE BELONGS ON ATLANTIS!'

'HE HAS THE EXPERIENCE THAT WE NEED!'

John walked into the corridor leading to Dr. Rush's labs, and immediately heard Colonel Young and Rush arguing about him.

'I will be going home,' John said loudly, running in between the two men. 'As soon as I can get there. We are in danger from the Asuran's there, and we need to protect ourselves. Me being here,' he indicated towards Rush. 'Is dangerous to Atlantis. I Need To Get Back.' He said, punctuating each of his last words.

Rush stared back at him, unreadable.

John turned to Colonel Young. 'Eli said you needed to see me?'

Everett nodded, and indicated that he should follow him.

XXX

Everett pulled them into an unused area of the ship. 'You need to be careful with Rush.'

'What do you mean?' John said carefully.

'He will try to stop you from leaving the Destiny.' Young said. 'He's an manipulative man. You can't trust him.'

John nodded. 'I know that.'

'You forget it though.' Young reminded him.

John stared at him for a minute in silence before saying, 'Don't presume to know me.'

He left, leaving Young to watch him leave.

XXX

John was walking through the ship, looking for Eli.

He gave up after a while, and just asked the nearest person. 'He'll be in the Kino room.' They told him.

'Thanks.'

It took him a further half an hour to actually find the Kino room.

He stood in the doorway watching Eli messing about with little ball camera things and felt laughter bubbling in his body.

Eli caught sight of him and dropped the balls, which floated around the room. 'Colonel Sheppard!'

'Hello Eli.' He said happily.

'What are you doing Eli?' John asked, walking into the room.

'Figuring out the Kino's.' Eli said excitedly.

'The what?' John asked nonplussed.

'Oh, they're floating camera's basically.' Eli explained.

'Cool.' John said smiling.

'Sit down and I'll show you.' Eli said.

John sat down and he didn't leave at all.

XXX

Soo, is there anything anybody would like added before John leaves back to Atlantis? I don't have anything in mind at the moment so I'll try to incorporate your ideas =D

Thanks for reading =D

Emily.


	4. Rush

John sat in the science lab. Bored.

He thought that after 5 years with Rodney he would know something about science.

Apparently he was wrong.

He let his head land on the consol, and Eli laughed watching him.

'You not the science type then?' Eli joked, standing up and moving to his console.

John looked up at him blearily and tried to glare. Unfortunately, due to Eli's grin, he failed miserably.

'Come on,' Eli said, motioning towards the door. 'You need rest. You're not going to get back to Atlantis in two weeks if you can't concentrate.'

John looked up, and found Rush glaring at them. 'You cannot leave now!'

Eli looked at him. 'Why?'

'Because he has two weeks! He needs to get home for Colonel Young.' Rush said.

John glared back at him. 'You're the one that wants me to stay.'

Rush stayed silent, and Eli looked between them and intervened. 'Right... Rush, you need to stay here, and John, _please, _just come with me!'

John relented from glaring at Rush and looked at his softer friend. 'Where do you want to go Eli?'

Eli looked at him happily, and John felt happy in the knowledge that he'd helped him.

'We'll come back in a bit Rush.' Eli turned and looked at him once he'd got to the door.

Rush didn't even answer.

XXXXX

Eli walked down the corridor, in his thoughts, when he bumped into somebody. 'Oh, I'm so sorry, I didn't even know where I was going!' he apologised.

The man he'd knocked down, didn't say anything, just glared at him and left him alone in the corridor.

XXXXX

Rush sat alone in his rooms. He had finally left the science lab place, after two days, to get some sleep.

A knock at his door interrupted him just as he was about to lie down.

He sighed and answered the door.

On the other side, John Sheppard stood.

He sighed internally this time, and moved out of the doorway to allow him in.

The other man hesitantly stepped into the room, stopping just in the doorway.

'I just wanted to talk to you.' John said after a few minute's silence.

'Shut the door then, and sit down, you're going to be here a while.' Rush said sarcastically.

'God! You sound just like Carson.' John murmured. 'You have the same accent, and it's so different.'

'Yes well, I am not, nor will I ever be Carson Beckett.' Rush said annoyed. 'What did you want to discuss?'

'I want to discuss you.' John said.

'What about me?'

'Young told me to avoid you, Eli told me to be careful around you, and generally people have told me not to go near you.' John said. 'I want to know why.'

Rush snorted slightly. 'Colonel Young.' He said, sitting on his bed. 'He hates me, and I hate him. I do not think that he is the right man for the job, and I was part of a force against him. Eli. Eli is different.' He said after a while.

'Yes, he is.' John agreed. 'He's the best person on this ship.'

'Maybe he is.' Rush commented. 'Eli is careful around everybody. You look at Eli and you don't suspect for a minute that he'd one of the most intelligent people here, and that is what he relies on. Apparently, just like you do.' Rush said, turning the conversation back to the black haired man.

'People underestimate you when you're a soldier.' John said levelly. 'If I told you that I passed MENSA, would you believe me?'

Rush laughed. 'You passed MENSA? I would never have suspected that.'

'Exactly.' John said. 'If you are up against an enemy, for example the Genii, then the best thing that can happen is that they underestimate you.' He looked away from Rush's Stargate coloured eyes. 'That's exactly what they did.'

'And you killed sixty of them single handed.' Rush commented.

'Yes.' John said harshly. 'All of them.'

Rush stared at him silently.

'That's what Eli does,' John carried on. 'He gets people to underestimate people, so that they don't think anything when they see him watching them, figuring out their secrets, and their uttermost desires. And he's good at it.'

Rush nodded. 'Yes, he is.'

John looked way and went to stand up, 'I shouldn't have come here, not now.'

Rush walked over to him, standing next to the door, like a predator going in for the kill.

'Maybe you should have.' He growled before capturing his lips.

John pushed on the scientist's arms, pushing him back, and he fell backwards, hitting the soft material of the bed, the colonel on top of him.

XXXXX

**Thanks for reading, =D**

**Emily.**


	5. Sex?

John woke up in an unfamiliar place and groaned.

'Where the hell am I this time?' he murmured to himself.

'You're in my quarters.'

He jerked upward, the blanket flying down to his waist. 'Rush?'

'Yes.'

'Did we... have sex?' John managed.

'I assume so yes.' Rush looked quite calm to John.

John let his body fall back to the bed.

XXXXX

Eli groaned, his head pounding. He moved slowly, trying to sit up with his eyes closed.

'Stay down!'

Eli grimaced, the loud voice cutting through his head like butter. 'What do you want?'

Opening his eyes, he saw the man he had walked into the other day, medium height, military, dark blue eyes, light brown-blond hair. Face set into a scowl.

'It's your fault we're here!' he hissed, leaning down to Eli's height. 'And you're going to pay!'

'How is it my fault?' Eli squeaked.

'You found the ninth chevron! You got us here!' the man hissed. 'You made me miss my family's funeral!'

'Funeral?'

The man shoved Eli back into the wall, and Eli vaguely recognised it as the hydroponics lab. 'They died because you made me come here!'

'That isn't my fault.' Eli said quietly.

'You're going to pay!' The marine yelled grabbing his shoulders and hauling him up against the wall. 'You're going to die!'

He leaned closer the Eli's ear before whispering, 'I'm going to be the one to end you're miserable life.'

The marine moved his hands from his shoulders to his neck and squeezed.

Eli chocked, clawing at the man's hands, trying to remove the hands. His movements slowed as black spots encroached the edge of his vision, and he tried to cry out but only came out as a wheeze which got rid of most of the oxygen he had.

Movement stilled as his brain ran out of oxygen, and his vision faded, and as he fainted, the hands around his neck loosened, and he heard bullets whizzing and what sounded like a body hitting the floor but Eli let go.

XXXXX

John sat by Eli's bedside holding his hand. His friend had nearly died, and where was he? With Rush.

John growled under his breath and stood up. He paced around the room and didn't see Rush entering the doorway and watching him.

'Pacing the room isn't going to help either you or Eli.' He said softly in a soft Scottish accent.

John spun around. 'He's my friend! I should have protected him!'

'You can't think like that!' Rush said, striding forward and grabbing his shoulders to make him look at him.

'Sergeant Lestro was mentally unbalanced.' Rush said slowly. 'His family died two weeks after he came onto the Destiny, and he thought that if he was there he could have saved them.'

'I know this Rush.' John said, glaring at the scientist. 'He used to be on Atlantis, he was stationed there before requesting a transfer back to Earth. I should have known his problems back then.'

'They haven't become apparent until now.' Rush said, letting go of his shoulders and moving to stand by Eli's bed. 'He'll be ok. He's strong.'

John moved back into the chair, and stared at the scientist sadly. 'I know. He's just like Rodney.'

'I think Dr. McKay is a bit more...' Rush struggled to find a word to describe the aforementioned scientist.

'Acerbic?' John said with a smirk.

Rush shrugged. 'That could be one of them.'

John stared at the bed.

Rush turned around. 'Stop being so sad.'

John was about to answer when he heard a moan from the bed.

'Eli?' he said, standing up and running to the bed. 'Eli? Are you ok?'

The scientist on the bed looked at him blearily. 'What happened?'

'You got attacked by a marine Eli.' John said gently.

Eli nodded before coughing. 'That's painful.' He gasped.

'You got strangled.' Rush informed him.

Eli turned his eyes to the older man. 'Who was it?'

'Sergeant Michael Lestro.' Rush said.

Eli nodded. 'I think I'm falling asleep.'

'Go to sleep then Eli.' John said grinning, 'We'll be here when you wake up.'

XXXXX

It was a week later and Eli was allowed out of the medic's view, and he went with John. 'I have something to give to you.'

John grinned at his recovering friend and followed him down a corridor close to where John's quarters were located.

Eli stopped him just he went into a room and said to him. 'Make sure nobody comes in.'

John nodded and lounged outside the doorway while Eli went in.

A few minutes passed before he came out again and Eli instructed him to go to his quarters.

XXXXX

'Right,' Eli said, once they were in Eli's room. 'You mustn't show this to anybody.'

John nodded, bemused.

Eli handed him a small wrapped package. 'You mustn't open this until you are back on Atlantis.'

John nodded. 'OK.'

'Promise me.'

John stared at him. 'I promise.'

XXXXX

'It's going to be six weeks tomorrow.' Rush said, as he and John lay in bed.

'I know.' John murmured.

'It's all going to change tomorrow.' Rush said.

'I know.' John murmured again.

Long after Rush had fallen asleep, John whispered. 'I'm sorry Nicholas.'

XXXXX

When Rush woke up the next morning, the other side of the bed was empty and cold, nothing of the other man remaining.

XXXXX

**Thank you for reading and for the waiting for the long wait I made you wait for!**

**Hope you like it =D**

**Emily**


	6. Atlantis

When John woke up, he rolled over to look at Rush and fell off of the bed.

He sat up and looked around at his surroundings. Atlantis. His room. Atlantis. Not the Destiny.

He looked around his room o look for his comm. Unit and finally found it on his bedside cabinet. He grabbed it and put it in his ear. 'Rodney. I'm back.'

XXXXX

John stood on the Eastern Pier three weeks later. He missed it. How else could he explain the longing to go back? He missed the ship, he missed the primitive Stargate, and he missed Eli. But he missed Rush most of all. Rush, with all the attitude of Rodney, and all the manipulative behaviour of a Wraith, and he missed him so much.

He didn't have a choice though; he couldn't leave his team again. Not like before.

Damned if he did and damned if he didn't.

He turned away from the bright blue of the sea. It was the same shade of his eyes.

XXXXX

John remembered the package two weeks after leaving the Pier. He opened it and sat cross legged on his bed in his quarters and held the black inscribed stone aloft in his hands. He closed his eyes and thought of the Destiny.

He opened his eyes again and saw himself in darkened quarters that he knew so well. He looked next to him and saw the sleeping man he had missed so much.

'Nicholas.' He called gently.

'Eli?' the sleeping man murmured. 'I'm sleeping so leave me alone. I'm not thinking about him.'

'You've been thinking about me Nicholas.' John said amused.

Rush jerked upwards. 'John? Is it really you?'

He grinned. 'Of course. Eli gave me a stone.'

Rush smirked sleepily. 'That's good.'

XXXXX

John opened his eyes again and saw his room. He smirked. 'Oh he'd have fun with this.' He thought.

'_I'll see you soon Nicholas.'_


End file.
